The invention discloses an adhesion eliminating structure of an inertial sensor and a method thereof. The structure comprises a driving device located in the movement direction of a mass block of the inertial sensor. The driving device fixedly installed relative to a stopping mechanism comprises an ejecting pin assembly making contact with the mass block. The driving device is arranged in the mode that when the mass block adheres to the stopping mechanism, the driving device moves, and the ejecting pin assembly is driven to separate the mass block from the stopping mechanism. According to the adhesion eliminating structure, after the mass block and the stopping mechanism adhere together, the driving device is controlled to move, and therefore the ejecting pin assembly can move in the direction of the mass block, finally, the mass block and the stopping mechanism are driven to be separated, adhesion elimination of the mass block is achieved, and the service life of the inertial sensor is prolonged. The adhesion eliminating structure can be designed by means of a redundant framework structure on the outer side of the mass block, and therefore the occupied area of a chip is not increased, and the overall size of the MEMS chip is not affected.